I'm looking to replace the 3.6V barrel batteries in my A2000 and 500. I'm not willing to do the diode hack to allow for the use of regular coin batteries (I need them more for other things), and computer store clerks simply look at me funny when I ask them about the barrel batteries.

According to this page, almost any 3.6V cordless phone battery pack will suffice as a replacement. Do they do a good job? Will they last as long between charges as the original battery does? Is there any brand or type in particular I should be looking for?

You should find an electronics shop that sells those components... I found one in my city called "Techics". They still sell those barrel type of batteries for about 4-5 euro. Just solder it to the mobo...